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PDBsum entry 2np0
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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2np0

 

 

 

 

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Contents
Protein chains
1289 a.a. *
15 a.a. *
Metals
_CA ×3
_ZN
_CL
Waters ×406
* Residue conservation analysis
PDB id:
2np0
Name: Hydrolase
Title: Crystal structure of the botulinum neurotoxin type b complexed with synaptotagamin-ii ectodomain
Structure: Botulinum neurotoxin type b. Chain: a. Synaptotagmin-2. Chain: b. Fragment: vesicular (residues 1-60). Synonym: synaptotagmin ii, sytii. Engineered: yes
Source: Clostridium botulinum. Organism_taxid: 1491. Strain: type b1_okra. Mus musculus. House mouse. Organism_taxid: 10090. Gene: syt2
Resolution:
2.62Å     R-factor:   0.188     R-free:   0.227
Authors: Q.Chai,J.W.Arndt,R.C.Stevens
Key ref:
Q.Chai et al. (2006). Structural basis of cell surface receptor recognition by botulinum neurotoxin B. Nature, 444, 1096-1100. PubMed id: 17167418 DOI: 10.1038/nature05411
Date:
26-Oct-06     Release date:   26-Dec-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10844  (BXB_CLOBO) -  Botulinum neurotoxin type B from Clostridium botulinum
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1291 a.a.
1289 a.a.
Protein chain
Pfam   ArchSchema ?
P46097  (SYT2_MOUSE) -  Synaptotagmin-2 from Mus musculus
Seq:
Struc: 		422 a.a.
15 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.3.4.24.69  - bontoxilysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevins, SNAP25 or syntaxin. No detected action on small molecule substrates.
      Cofactor: Zn(2+)

 

 
DOI no: 10.1038/nature05411 Nature 444:1096-1100 (2006)
PubMed id: 17167418  
 
 
Structural basis of cell surface receptor recognition by botulinum neurotoxin B.
Q.Chai, J.W.Arndt, M.Dong, W.H.Tepp, E.A.Johnson, E.R.Chapman, R.C.Stevens.
 
  ABSTRACT  
 
Botulinum neurotoxins (BoNTs) are potent bacterial toxins that cause paralysis at femtomolar concentrations by blocking neurotransmitter release. A 'double receptor' model has been proposed in which BoNTs recognize nerve terminals via interactions with both gangliosides and protein receptors that mediate their entry. Of seven BoNTs (subtypes A-G), the putative receptors for BoNT/A, BoNT/B and BoNT/G have been identified, but the molecular details that govern recognition remain undefined. Here we report the crystal structure of full-length BoNT/B in complex with the synaptotagmin II (Syt-II) recognition domain at 2.6 A resolution. The structure of the complex reveals that Syt-II forms a short helix that binds to a hydrophobic groove within the binding domain of BoNT/B. In addition, mutagenesis of amino acid residues within this interface on Syt-II affects binding of BoNT/B. Structural and sequence analysis reveals that this hydrophobic groove is conserved in the BoNT/G and BoNT/B subtypes, but varies in other clostridial neurotoxins. Furthermore, molecular docking studies using the ganglioside G(T1b) indicate that its binding site is more extensive than previously proposed and might form contacts with both BoNT/B and synaptotagmin. The results provide structural insights into how BoNTs recognize protein receptors and reveal a promising target for blocking toxin-receptor recognition.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: The structure of BoNT/B–Syt-II recognition domain complex. Ribbon diagram of BoNT/B–Syt-II recognition domain complex, with subdomains of BoNT/B labelled as light chain (orange), H[N] (green), H[CN] (grey), and H[CC] (blue). The Syt-II recognition domain (residues 45–59, magenta) forms an -helix when complexed with BoNT/B. 		Figure 2.
Figure 2: Interaction between the H[CC] domain of BoNT/B and the recognition domain of Syt-II. a, Binding interface on BoNT/B (circled in dashed line) reveals hydrophobic groove (green, hydrophobic surface). b, Close-up view of the binding interface of Syt-II (magenta) and BoNT/B (light blue) by rotating 90° around the x axis. c, Truncation mutants of Syt-II were tested for BoNT/B binding activity. d, Point mutants of Syt-II were tested for BoNT/B binding activity. e, f, Various synaptotagmin mutants, in which residues within the recognition domain were interconverted between Syt-II and Syt-I, were tested for BoNT/B binding activity. WT, wild type; GST, glutathione S-transferase.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 444, 1096-1100) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20138889 J.Dong, A.A.Thompson, Y.Fan, J.Lou, F.Conrad, M.Ho, M.Pires-Alves, B.A.Wilson, R.C.Stevens, and J.D.Marks (2010).
A single-domain llama antibody potently inhibits the enzymatic activity of botulinum neurotoxin by binding to the non-catalytic alpha-exosite binding region.
  J Mol Biol, 397, 1106-1118.
PDB code: 3k3q
20704566 J.Strotmeier, K.Lee, A.K.Völker, S.Mahrhold, Y.Zong, J.Zeiser, J.Zhou, A.Pich, H.Bigalke, T.Binz, A.Rummel, and R.Jin (2010).
Botulinum neurotoxin serotype D attacks neurons via two carbohydrate-binding sites in a ganglioside-dependent manner.
  Biochem J, 431, 207-216.
PDB codes: 3obr 3obt
20233039 M.Montal (2010).
Botulinum neurotoxin: a marvel of protein design.
  Annu Rev Biochem, 79, 591-617.  
20571899 M.Z.Atassi, B.Z.Dolimbek, L.E.Steward, and K.R.Aoki (2010).
Inhibition of botulinum neurotoxin a toxic action in vivo by synthetic synaptosome- and blocking antibody-binding regions.
  Protein J, 29, 320-327.  
20877571 N.Gul, L.A.Smith, and S.A.Ahmed (2010).
Light chain separated from the rest of the type a botulinum neurotoxin molecule is the most catalytically active form.
  PLoS One, 5, e12872.  
20219474 P.Stenmark, M.Dong, J.Dupuy, E.R.Chapman, and R.C.Stevens (2010).
Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.
  J Mol Biol, 397, 1287-1297.
PDB code: 2vxr
20169001 Y.Fujinaga (2010).
Interaction of botulinum toxin with the epithelial barrier.
  J Biomed Biotechnol, 2010, 974943.  
19164566 A.Fischer, Y.Nakai, L.M.Eubanks, C.M.Clancy, W.H.Tepp, S.Pellett, T.J.Dickerson, E.A.Johnson, K.D.Janda, and M.Montal (2009).
Bimodal modulation of the botulinum neurotoxin protein-conducting channel.
  Proc Natl Acad Sci U S A, 106, 1330-1335.  
19650874 A.Rummel, K.Häfner, S.Mahrhold, N.Darashchonak, M.Holt, R.Jahn, S.Beermann, T.Karnath, H.Bigalke, and T.Binz (2009).
Botulinum neurotoxins C, E and F bind gangliosides via a conserved binding site prior to stimulation-dependent uptake with botulinum neurotoxin F utilising the three isoforms of SV2 as second receptor.
  J Neurochem, 110, 1942-1954.  
19111565 M.Montal (2009).
Translocation of botulinum neurotoxin light chain protease by the heavy chain protein-conducting channel.
  Toxicon, 54, 565-569.  
19476346 Z.Fu, C.Chen, J.T.Barbieri, J.J.Kim, and M.R.Baldwin (2009).
Glycosylated SV2 and gangliosides as dual receptors for botulinum neurotoxin serotype F.
  Biochemistry, 48, 5631-5641.
PDB codes: 3fuo 3fuq
19014598 A.C.Doxey, M.D.Lynch, K.M.Müller, E.M.Meiering, and B.J.McConkey (2008).
Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster.
  BMC Evol Biol, 8, 316.  
18032388 A.Fischer, C.Garcia-Rodriguez, I.Geren, J.Lou, J.D.Marks, T.Nakagawa, and M.Montal (2008).
Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy.
  J Biol Chem, 283, 3997-4003.  
18606570 A.Varki (2008).
Sialic acids in human health and disease.
  Trends Mol Med, 14, 351-360.  
17967862 C.L.Pier, W.H.Tepp, M.Bradshaw, E.A.Johnson, J.T.Barbieri, and M.R.Baldwin (2008).
Recombinant holotoxoid vaccine against botulism.
  Infect Immun, 76, 437-442.  
18815274 M.Dong, H.Liu, W.H.Tepp, E.A.Johnson, R.Janz, and E.R.Chapman (2008).
Glycosylated SV2A and SV2B mediate the entry of botulinum neurotoxin E into neurons.
  Mol Biol Cell, 19, 5226-5237.  
18693250 M.Galloux, H.Vitrac, C.Montagner, S.Raffestin, M.R.Popoff, A.Chenal, V.Forge, and D.Gillet (2008).
Membrane Interaction of Botulinum Neurotoxin A Translocation (T) Domain: THE BELT REGION IS A REGULATORY LOOP FOR MEMBRANE INTERACTION.
  J Biol Chem, 283, 27668-27676.  
18070903 M.R.Baldwin, W.H.Tepp, A.Przedpelski, C.L.Pier, M.Bradshaw, E.A.Johnson, and J.T.Barbieri (2008).
Subunit vaccine against the seven serotypes of botulism.
  Infect Immun, 76, 1314-1318.  
18704164 P.Stenmark, J.Dupuy, A.Imamura, M.Kiso, and R.C.Stevens (2008).
Crystal structure of botulinum neurotoxin type A in complex with the cell surface co-receptor GT1b-insight into the toxin-neuron interaction.
  PLoS Pathog, 4, e1000129.
PDB codes: 2vu9 2vua
17666397 A.Fischer, and M.Montal (2007).
Crucial role of the disulfide bridge between botulinum neurotoxin light and heavy chains in protease translocation across membranes.
  J Biol Chem, 282, 29604-29611.  
18158333 M.Dong, W.H.Tepp, H.Liu, E.A.Johnson, and E.R.Chapman (2007).
Mechanism of botulinum neurotoxin B and G entry into hippocampal neurons.
  J Cell Biol, 179, 1511-1522.  
17203068 M.R.Baldwin, J.J.Kim, and J.T.Barbieri (2007).
Botulinum neurotoxin B-host receptor recognition: it takes two receptors to tango.
  Nat Struct Mol Biol, 14, 9.  
17167419 G.Schiavo (2006).
Structural biology: dangerous liaisons on neurons.
  Nature, 444, 1019-1020.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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